Well, WTF from South Africa did that. And ST2 banned him....and i agree with that...if i`d caught someone selling his trains right at the end just to score more points , i`d ban too.
As for your idea of penalizing late entries...I just got one question....WHY?
It`s hard enough for a player having to catch up....but being penalized....seems totally unfair...and also will ruin the number of players that actually try to catch up even if the oponent is far ahead.
Beside...xor is right...as soon as he changes the calculation formula ,a new thread will appear asking him to get back to the old formula.
dont worry alex
my pride of having a nice system full of trains is bigger then my will to score an extra 50 points 
i think the case with WTF was before we had the logics that vehicles decrease your score and he did the opposite: buy lots of unused trains short before end. this boosted both his company value and the score. that's not possible anymore.
about the problem you described: you forget that you can't do that to the full extend. if you almost reached the goal and now sell most of your trains you will also lose a LOT of company value and suddenly reaching the goal isn't so close anymore. and without your trains you will also lose a lot of income so you won't get to the goal soon. and if you don't win until the end of the quarter all your performance scores will also drop. so yes, this can be used for cheating, but not as easily and as much as you might think.
also you can get caught easily. the cheating can even be seen 2 months later just by looking at the database. because i see with how many trains you finished and how long you took. with your trick your ratio of game length to the number vehicles you had will be obviously differing from the average, probably by something as high as 500%. i already have plans to search for such anomalies automatically and if we find your account ALL your scores will be reset. if you're lucky. otherwise you also get a ban and/or the whole account deleted.
so the risk is quite high.
i hope this all doesn't sound to you like i don't want to do changes to the score algorithm at all. it's just that it's not an easy thing and for every change with a positive effect on one side you can get a negative effect on the other (in worst case without noticing it). additionally a bigger change to the score system also means a score reset - obviously something we don't want to do too often. more explanations on that and also some good ideas are on this thread:
http://www.n-ice.org/openttd/forum/index.php?topic=54.0
